tbuckley/cabot-search huggingface dataset:
EXTH-78. CRISPROFF EPIGENOME EDITING AND FUNCTIONAL GENOMICS DEFINE MEDIATORS OF CHEMOTHERAPY RESISTANCE IN GLIOBLASTOMA
Authors: Katie Lin, Laine Goudy, Joanna Pak, Kyla Foster, Emily Payne, Tomoko Ozawa, John de Groot, Harish Vasudevan, David Raleigh, Luke Gilbert, Mitchel Berger, John Liu
Journal: Neuro-Oncology (2023)

Abstract Alkylating chemotherapies exhibit survival benefit for patients with glioblastoma (GBM). CRISPRoff is a programmable epigenetic memory writer that stably and heritably silences genes through DNA methylation. Epigenetic silencing of MGMT via promoter methylation predicts response to chemotherapy and is prognostic for overall survival. Here, we performed epigenome editing using CRISPRoff to stably silence MGMT through induced promoter methylation as a therapeutically tractable approach for potentiating GBM to chemotherapy. We then used genome-wide CRISPR interference (CRISPRi) screens to broadly define novel chemosensitizing targets of GBM cells. Epigenome editing was performed through electroporation of CRISPRoff mRNA and sgRNAs into MGMT hypomethylated GBM cell lines (LN18 and T98G) and primary GBM cells. Whole genome bisulfite sequencing, RT-qPCR, and western blot assessed gene silencing. Cell viability assays measured drug sensitivity. GBM xenografts with CRISPRoff-induced silencing of MGMT were intracranially transplanted in mice and treated with temozolomide. Genome-wide functional genomics screens were performed using CRISPR interference. CRISPRoff against MGMT reduced MGMT mRNA and protein levels by 99.97%, generating up to 150-fold sensitization to temozolomide and 9-fold sensitization to lomustine in GBM cells. Silencing remained stable and heritable in clonally isolated GBM cells at 145 days after transient delivery of CRISPRoff, and gene repression and drug sensitization were equivalent to Cas9-mediated homozygous deletion of MGMT in vitro and in vivo. CRISPRoff of MGMT in intracranial xenografts exhibited significant reduction in tumor growth with temozolomide treatment compared to temozolomide treatment with control CRISPRoff (p = 0.0047). CRISPRi screens validated MGMT and defined 266 and 238 additional modifiers of temozolomide and lomustine response, respectively, including the ATR (BRCA2), DNA repair (REV1), cell cycle (PSMD13), and Fanconi anemia pathways (FANCI, FANCD2). In summary, we integrate targeted epigenome editing with unbiased genome-wide approaches to establish a novel discovery and therapeutic platform against glioblastoma.
CTNI-80. INTUITT-NF2, AN ADAPTIVE PLATFORM-BASKET TRIAL FOR <i>NF2</i>-RELATED SCHWANNOMATOSIS PATIENTS WITH PROGRESSIVE SCHWANNOMAS, MENINGIOMAS, AND EPENDYMOMAS: PRIMARY OUTCOME OF THE BRIGATINIB TREATMENT ARM
Authors: Scott R Plotkin, Dusica Babovic-Vuksanovic, Christine Dinh, Geoffrey Fell, Vanessa Merker, Phioanh Nghiemphu, Lorenzo Trippa, Kaley Yohay, Jaishri Blakeley
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION NF2-related schwannomatosis (NF2-SWN) predisposes affected individuals to vestibular schwannomas (VS), non-vestibular schwannomas (NVS), meningiomas, and ependymomas. The rarity of NF2-SWN and the presence of multiple tumor types has impeded clinical trials. We conducted a multi-center, adaptive, platform-basket trial to screen multiple drugs against progressive NF2-SWN tumors. We report the final analysis of the first treatment arm with brigatinib, an oral ALK inhibitor that inhibits multiple tyrosine kinases. METHODS This study enrolled participants ≥ 12 years with NF2-SWN and progressive target tumors (baskets: VS, NVS, meningioma, or ependymoma Radiographic response (RR) was defined as ≥ 20% decrease in target tumor volume from baseline. The primary outcome was RR rate. Secondary outcomes included safety, hearing response, and RR in non-target tumors. Tumor response was evaluated by MRI every 3 months in year 1 and every 6 months thereafter. In stage 1, 20 participants received brigatinib 180 mg daily. Interim analysis suggested activity in NVS and meningioma. Thus, an additional 20 participants with progressive meningioma or NVS were enrolled in stage 2. RESULTS Forty participants (median age 26 years, 12 pediatric, 28 female) were treated. Prior treatment included surgery (90%), radiation therapy (20%) and chemotherapy (55%). Target tumors included 10 VS, 9 NVS, 19 meningiomas, and 2 ependymomas. Overall RR rate was 10% for all target tumors (22% for non-VS, 11% for meningioma, 0% for VS, and 0% for ependymomas). There were no grade 4 or 5 treatment-related adverse events (AEs). The most common AEs were diarrhea (63%), nausea (40%), muscle cramps (33%), increased LDH (35%), increased AST (33%), and increased ALT (23%). CONCLUSION Brigatinib treatment was associated with RR in NVS and meningiomas in a heavily pretreated cohort of participants with progressing NF2-SWN tumors. This novel design provides unique ability to assess treatments for hereditary syndromes with multiple primary tumors.
TMIC-19. TARGETING TUMOR-MYELOID CELL SYMBIOSIS IN GLIOBLASTOMA
Authors: Peiwen Chen
Journal: Neuro-Oncology (2023)

Abstract Heterotypic interactions across diverse cell types of the tumor microenvironment can enable tumor progression and offer points for potential therapeutic intervention. Employing glioblastoma (GBM), a lethal form of brain tumor in adults, as a model system, we sought to (i) understand the nature of specific oncogenic signals in glioma cells that affects myeloid cell biology; (ii) identify myeloid cell factors which may support glioma growth and survival, (iii) develop novel therapeutic strategies targeting the tumor-myeloid cell symbiosis; and (iv) investigate whether blockade of this symbiosis can overcome the primary resistance of immunotherapy. Specifically, the novel oncogenic signals (e.g., CLOCK and TFPI2) and myeloid cell components of microglia and myeloid-derived suppressor cells will be discussed and highlighted. The findings from our studies demonstrate that the newly identified context-dependent tumor-myeloid cell symbiotic interactions not only promote tumor progression but also induce immune checkpoint inhibitor (ICI) therapy resistance in GBM. Thus, our studies provide novel therapeutic targets and offer a great potential to overcome immunotherapy resistance in GBM.
DDDR-12. ESTABLISHING A SAFE AND EFFICACIOUS ANTI-GLIOBLASTOMA THERAPY
Authors: Carmen del Genio, Sidney Nguyen, Zachary Shalit, Elizabeth Pizzi, Bamlak Messay, Dominique Fontaine, Yujia Shentu, Heather Wishart, James Ford, Glenn Micalizio, Arti Gaur
Journal: Neuro-Oncology (2023)

Abstract Glioblastomas (GBM) are primary brain tumors that are among the most treatment-resistant human cancers with a median survival of only 14 months and a 5-year survival rate of less than 5%. The standard-of-care for GBM has remained unchanged for two decades and more than half of newly diagnosed patients do not see any therapeutic benefit with existing regimens. Due to a 25:1 failure ratio in developing new brain tumor treatments, the FDA has approved only four drugs against GBM in the past three decades. This failure in clinical development can be attributed primarily to severe toxic side effects, the inability of most compounds to cross the blood brain barrier (BBB) and use of pre-clinical models that do not represent the molecular heterogeneity of GBM. To fulfill this unmet need for curative treatments we are developing an anti-GBM therapy in a clinically relevant patient-derived in vivo model and selectively targeting estrogen receptor-beta (ERβ) using ent-28, a novel, highly selective and potent agonist of ERβ. ent-28 has 9000-fold higher selectivity for ERβ compared to estrogen, or 17β- estradiol; precluding non-specific binding of ERα. ent-28 inhibits the proliferation of GBM patient-derived adherent and stem cells but not of human astrocytes and neural progenitor cells in vitro. More critically, ent-28 is not toxic and does not have off- target side effects in immune-competent mice even after one year long chronic treatment. These data have enabled us to further establish that using an oral route of delivery, ent-28 crosses the BBB and significantly reduces or ablates intra-cranial, orthotopically implanted GBM patient-derived xenografts, resulting in increased survival of ent-28 treated mice. Pre-clinical data will be presented on safety, pharmacokinetics, metabolic stability, in vivo efficacy, mechanism of action and species rationalization for this novel, ERβ agonist that is being developed as an anti-GBM therapy.
RADT-10. BRAINSTEM METASTASES TREATED WITH STEREOTACTIC RADIOSURGERY: MASKED VS. FRAMED IMMOBILIZATION
Authors: Sabrina Begley, Anuj Goenka, Michael Schulder
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Patients with brainstem metastases (BSM) have minimal surgical options due to high-risk anatomy. To review our efficacy treating BSM using Gamma Knife stereotactic radiosurgery (GK SRS), we compared results based on the utilization of mask-fixation (MF) or frame-fixation (FF). METHODS Data were retrospectively collected for 32 patients. Follow-up data for 49 lesions were analyzed for local control rate (LCR) and objective response rate (ORR). RESULTS Primary cancers included lung, breast, and melanoma; most lesions were pontine. MF was used in 18 patients. Average tumor volume was 0.99 cm3 (0.005 – 13.3 cm3). 39 lesions were treated with single fraction 16 Gy. 10 lesions were treated in 3-5 fractions with mean dose of 22.5 Gy. Mean follow-up was 14.2 months (1.2 - 48.2 months). 1-year LCR was 94.7%. ORR at last follow-up did not differ between MF vs. FF (p = .81). Average reduction of lesion volume at 6 and 12 months did not differ between MF vs. FF (64% vs 45%, p = .77; 70% vs 77%, p = .78). Failure occurred in a pontine colorectal cancer metastasis mask-immobilized for treatment with 14 Gy. CONCLUSIONS SRS for BSM achieved high LCR despite variability in tumor size and histology with no significant difference between MF vs. FF. Although trials have historically excluded patients with BSM, our data support SRS as a safe and efficacious treatment. This is the first study showing that MF provides equivalent, successful outcomes when compared to FF for patients with BSM.
INNV-23. HEALTH AND HEALTHCARE FACTORS THAT SHAPE THE GLIOMA PATIENT EXPERIENCE THROUGHOUT THE CANCER CONTINUUM: THE VALUE OF CARE COORDINATION AND COMMUNICATION
Authors: Alayna Ernster, Mollie Canzona, Fang-Chi Hsu, Kathryn Weaver, Angelica Hutchinson, Glenn Lesser, Kristin Houston, Alexandria Marshall, Alisha DeTroye, Roy Strowd
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Cognitive or communication deficits from glioma may pose challenges in patients’ ability to manage their illness and navigate the healthcare system. Disease-specific barriers must be overcome to achieve patient-centered care and shared-decision making. This study identified health and healthcare factors that enhance or complicate the patient experience throughout the glioma-cancer continuum. METHODS Semi-structured interviews (N=8) or focus groups (N=6) were conducted in-person or via phone call with 23 glioma patients at any point during their cancer care. The constant comparative method was used to identify themes illustrating the healthcare factors that shape the glioma patient experience. RESULTS Three themes that facilitate the healthcare experience and six themes that complicate the healthcare experience were identified. Facilitating themes included (1) free exchange of information with healthcare providers (HCP), (2) HCP expectation setting and efforts to support patient agency, and (3) HCP relationship building efforts. Complicating themes included (1) early attempts to address initial symptoms in healthcare settings, (2) patient perception of initial symptoms, (3) long wait times and time-intensive appointment schedules, (4) accessing and navigating procedures for appointments and multiple locations, (5) timing and delivery of information during treatment, and (6) mixed messages about prognosis and treatment recommendations. DISCUSSION Health and healthcare factors that influence the glioma patient experience are concentrated around patients’ relationships and communication with HCP and the logistics of cancer care delivery. Logistical barriers to care delivery negatively affect the patient experience and highlight the need for interventions that aim to streamline care delivery, help patients manage care, fulfill healthcare information needs, and enhance team-based cross-disciplinary communication.
PATH-18. MORE UNUSUAL FEATURES IN H3 K27M-MUTANT GLIOMAS
Authors: B K DeMasters, Samuel Guzman, David Ormond
Journal: Neuro-Oncology (2023)

Abstract Diffuse midline glioma, H3 K27M-altered, WHO grade 4 is an infiltrating midline glioma; however, H3 K27M mutation can also be seen in midline circumscribed, non-infiltrating gliomas and rarely in non-midline tumors. We report 2 unusual examples. A 37-year-old female developed a right posterior frontal infiltrating glioma; resection showed infiltrative tumor with brisk mitotic activity, elevated MIB-1 (20%), negative p53 expression, ATRX retention, but no necrosis or microvascular proliferation. Molecular workup showed neither IDH1/2/TERT promoter mutations or co-deletion 1p, 19q; further testing showed gain of whole chromosome 7 + loss of whole chromosome 10, meeting molecular criteria for glioblastoma. Recurrent tumor 2 years later in the same area prompted re-resection again of infiltrating tumor devoid of necrosis or microvascular proliferation; molecular testing now revealed a H3F3A (p.K28M) mutation. Both tumors showed protein expression by H3 K27M IHC+. She succumbed post-therapy at 3 ½ years. A 30-year-old woman developed a circumscribed, non-enhancing third ventricular mass; resection demonstrated circumscribed, non-infiltrating glioneuronal tumor with monotonous rounded tumor nuclei, synaptophysin IHC+, negative GFAP, H3 K27M IHC+, and low MIB-1. Molecular testing identified alterations in H3F3A p. K28M and FGFR1 p.N546K. She was treated, but lost to follow-up, until she re-presented 5 years later with hemorrhagic left frontal lobe tumor contiguous with the midline, with dorsal midbrain and 4th ventricular involvement. After resection, tumor now showed infiltrative features, necrosis and microvascular proliferation, diffuse GFAP IHC+, retention of nuclear ATRX, p53 (20%), MIB-1 (22%), and H3 K27M IHC+. New tumor had no FGFR1 alteration or PDGFRA amplification to suggest radiation-induced tumor, instead manifesting PTPRZ1-MET fusion. She survives at 5 years. These cases offer new insights into survival of a non-midline example and transformation of a circumscribed, non-infiltrating tumor to secondary infiltrating H3 K27-altered tumor with new molecular alterations, possibly representing second independent tumor development.
NCMP-15. AMYLOID-BETA AND TAU-PATHOLOGY IN THE GLIOMA VICINITY
Authors: Lisa Greutter, Yelyzaveta Miller-Michlits, Lisa Schnitzenlehner, Sigrid Klotz, Elena Krause, Stephan Platzek, Barbara Kiesel, Georg Widhalm, Peter Stepper, Karl-Heinz Nenning, Georg Langs, Bernhard Baumann, Adelheid Woehrer
Journal: Neuro-Oncology (2023)

Abstract With aging societies the incidences of brain cancer and neurodegenerative disease are increasing. Although biological associations were suggested between glioma and Alzheimer's disease (AD), the rate of comorbidity is ill-defined. We here screened the tumor-adjacent cortex of a representative patient cohort for tau and Amyloid-beta deposits and correlated the results with imaging biomarkers. A total of 290 patients (37 astrocytoma, IDH-mutant, CNS-WHO grades 2-4, median-age: 39; 48 oligodendroglioma, IDH-mutant and 1p-19q-co-deleted, CNS-WHO grades 2-3, median-age: 50; 205 glioblastoma, IDH-wildtype, median-age: 65) were included. Whole-slide quantifications were performed using a digital pathology pipeline based on Matlab and QuPath codes. For a subset of 48 patients with glioblastoma 280 longitudinal MRI volumes were available for segmentation and volumetric analysis of tumor ipsi- and contralateral hippocampuses. Overall, 160 patients (55%) displayed Amyloid-beta and/or tau-pathology in tumor-adjacent cortex. AD protein deposits correlated significantly with age (p&amp;lt; 0.001), and showed topographic variability across brain regions. Amyloid-beta plaques were commonly observed in the occipital cortex in glioblastoma (50%, n= 10/20), while tau-pathology was commonest in the temporal lobe in both IDH-mutant and -wildtype tumors (71%, n= 10/14; 56% n= 44/79). Remarkably, isolated tau-pathology was more prevalent in IDH-mutant glioma (48% vs. 18%, p&amp;lt; 0.001, median age: 45). Median cell density in tumor-infiltrated cortex was highest in glioblastoma (1895 cells/mm²), and associated with reduced neuronal counts and AD protein deposits (p&amp;lt; 0.001). In glioblastoma, hippocampal atrophy correlated with AD-type pathology at time of diagnosis and remained stable during follow-up in the majority of patients. In sum, our data suggests frequent co-morbidity of glioma and AD-type pathology, which increases with age. Isolated tau-pathology was more pronounced in IDH-mutant tumors. In tumor-adjacent cortex, increased tumor cell infiltration paralleled neuronal loss and diminished AD-type pathology.
DDDR-11. IDENTIFYING NEW VULNERABILITIES TO TARGET PEDIATRIC LOW-GRADE GLIOMA
Authors: Anna Borgenvik, Sean Misek, Jens Maile, Dana Novikov, Sher Bahadur, April Apfelbaum, Eric Morin, Alexandra Condurat, Elizabeth Gonzales, Kevin Zhou, Amy Goodale, Tanaz Abid, Zohra Kalani, Federica Piccioni, Keith Ligon, Rameen Beroukhim, Nicole Persky, David Jones, David Root, Pratiti Bandopadhayay
Journal: Neuro-Oncology (2023)

Abstract Pediatric low-grade gliomas (pLGGs) are the most common solid tumors in children and are associated with devastating lifelong morbidities and mortality. Recent genomic profiling efforts have revealed that these tumors are largely driven by single-driver events that activate MAPK signaling. These insights have led to early clinical trials evaluating the role of MAPK inhibitors for these children with promising initial results. However, pLGGs are not cured by MAPK inhibitors, and tumors often rapidly rebound upon cessation of treatment. Therefore, continuous dosing of these inhibitors is required throughout a child’s development–often with significant and potentially permanent toxicities. In addition, 30-40% of tumors do not respond to MAPK inhibition, indicating primary resistance. We hypothesized that pediatrlc low-grade gliomas may also harbor additional dependencies beyond the MAPK pathway that may represent potential therapeutic targets. To address this, we generated isogenic neural stem cell models that expressed pLGG relevant oncogenes (BRAF family members, FGFR family members and MYB transcription factors, and subjected them to genome-scale CRISPR-cas9 screens. Compared to vector controls, pLGG models exhibited genetic dependencies on pathways that included regulators of cell-cycle and differentiation, in addition to genes involved in regulating the mTOR and MAPK pathways. Cell lines expressing MYB family transcription factors also harbored dependencies on genes involved in the DREAM complex. Together, these genes and pathways represent potential targets for combination treatments with MAPK pathway inhibitors for the treatment of pediatric low-grade gliomas.
QOL-17. SLEEP QUALITY DIMENSIONS IN LOW AND HIGH-GRADE GLIOMA SURVIVORS
Authors: Erica Chen, Chencai Wang, Lucy Wall, Nicholas Cho, Benjamin Ellingson, Timothy Cloughesy, Albert Lai, Robert Chong, Kathleen Van Dyk, Phioanh Nghiemphu
Journal: Neuro-Oncology (2023)

Abstract In this study, we examined the relationship between sleep disturbance and tumor grades in a group of low-grade (LGG; grade I-II) and high-grade glioma (HGG; grade III-IV) survivors &amp;lt; 1 to 10+ years from initial diagnosis. 42 glioma survivors completed the Pittsburgh Sleep Quality Index (PSQI). We examined frequency of poor sleep quality (defined as PSQI &amp;gt;5) and compared global PSQI between LGG and HGG groups. We obtained high-resolution T1 weighted images from a subset of 24 patients for gray matter volume analyses. The sample was predominantly male (66%) and Caucasian (82%). Of the 42 participants, 31% (n = 13) had LGG and 69% (n = 29) had HGG. 60% (n = 25) of all participants had poor sleep quality, with no differences observed between LGG and HGG. There were no differences between groups in age, education, measures of depression and anxiety, or general health-related quality of life (MOS SF-36). A Mann-Whitney U test indicated that there was no significant difference in global PSQI scores between LGG (Mdn = 4) and HGG groups (Mdn = 6), U = 239, p = .254. Sleep quality was not associated with time since diagnosis for either LGG (r = .108, p = .724) and HGG groups (r=-.058, p = .762). Whole brain vertex-wise comparison revealed smaller gray matter volumes in patients with poor sleep quality versus good sleep quality in the isthmus cingulate, cuneus, and precuneus of the left hemisphere (p &amp;lt; 0.05). Our analyses suggest that sleep quality is important to assess in glioma survivors of any grade and at any time since diagnosis. Poor sleep in glioma survivorship could be associated with structural differences in brain regions sensitive to sleep problems in other populations. Given the high rate of sleep disturbance, further study is warranted to better understand risk and develop targeted interventions.
EXTH-21. FKBP38 REGULATES SELF-RENEWAL AND SURVIVAL OF GBM NEUROSPHERES
Authors: Aimee Dowling, Stuart Walbridge, Celine Ertekin, Jean-Paul Bryant, Eric Kohut, Ashis Chowdhury, Desmond Brown, John Heiss, Yeshavanth Kumar Banasavadi-Siddegowda
Journal: Neuro-Oncology (2023)

Abstract Glioblastoma (GBM) is the most common malignant primary brain tumor. The outcome is dismal, despite the multimodal therapeutic approach that includes surgical resection followed by radiation and chemotherapy. The quest for novel therapeutic targets to treat GBM is underway. FKBP38, a member of the immunophilin family of proteins, is a multidomain protein that plays an important role in the regulation of cellular functions including apoptosis and autophagy. In this study, we tested the role of FKBP38 in GBM tumor biology. Expression of FKBP38 is upregulated in the patient-derived primary GBM neurospheres (GBMNS) compared to normal human astrocytes. Attenuation of FKBP38 expression decreased the viability of GBMNS and increased the caspase 3/7 activity indicating that FKBP38 is required for the survival of GBMNS. Further, the depletion of FKBP38 significantly reduced the number of neurospheres that were formed implying that FKBP38 regulates the self-renewal of GBMNS. Also, the transient knockdown of FKBP38 increased the LC3-II/I ratio suggesting the induction of autophagy with the depletion of FKBP38. Further investigation showed that the negative regulation of autophagy by FKBP38 in GBMNS is mediated through the JNK/C-Jun-PTEN-AKT pathway. In vivo, FKBP38 depletion significantly extended the survival of tumor-bearing mice. Overall, our results suggest targeting FKBP38 imparts an anti-GBM effect by inducing apoptosis and autophagy and thus can be a potential therapeutic target for GBM therapy.